Coming up a 1/2 gal short just means you have a few less beers when you bottle. No problem. If your efficiency was where you expected then you should be a couple points higher than you expected.
Second if you did not make a starter then it is likely that your fermentation will not take off, especially if you did not have enough O2 in the wort. Shaking the carboy for about 5min should do the trick, at 1min you are a little short. This just means that the yeast will reproduce less and will ferment with a smaller population than ideal. This results in a slower ferment and perhaps a few more esters.
The beer will be fine but a starter and better aeration will improve the results next time.

Shaking is good before you add yeast, as it aerates the wort. But once the yeast has been pitched you want to leave it alone. One slight exception would be if you get a stuck fermentation - then you could very gently stir the wort with a sanitised spoon, to rouse the yeast. But that's not what you have in this case, so it'd be best to leave it. Your beer will be fine.